Many aspects of mammalian physiology and behavior are driven by an intrinsic timekeeping system that has an important role in synchronizing various biological processes within an organism and coordinating them with the environment. It is believed that deregulation of this coordination may cause the development of various pathologies. However, recent studies using mice deficient in individual components of the circadian system clearly demonstrated more complex interaction of the circadian system with various biological processes. The growing amount of evidence suggests that in addition to their roles in the core clock mechanism, some of the components of the molecular oscillator are involved in modulation of such diverse physiological processes as response to genotoxic stress, regulation of the cell cycle, aging, and carcinogenesis. These new data provide a mechanistic link between deregulation of the circadian system and/or some of its core components and the development of various pathologies, suggesting novel strategies for the disease treatment and prevention.